rs6526555

chrX-26351782-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.406 in 110,829 control chromosomes in the GnomAD database, including 8,109 homozygotes. There are 13,218 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.41 (8109 hom., 13218 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.406 AC: 44953 AN: 110774 Hom.: 8099 Cov.: 23 AF XY: 0.399 AC XY: 13167 AN XY: 33034

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.399

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.406 AC: 45017 AN: 110829 Hom.: 8109 Cov.: 23 AF XY: 0.399 AC XY: 13218 AN XY: 33099

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.533

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.402

Alfa AF: 0.281 Hom.: 10939

Bravo AF: 0.443

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.3
Dann	Benign	0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6526555; hg19: chrX-26369899;